Cycles - Baking Transparent Background
It is currently not possible to bake directly to an alpha channel as you mention. 

https://blender.stackexchange.com/a/41904/28015

There are workarounds, though, like you could bake only an emission shader of the masking (in this case you already have the mask so there's no need for that), then make it the alpha channel in the compositor.



Here is the blend:



Just bake the texture, update the compositor, and finally, go the the viewer node in the uv editor.